Contacts of the strand formed by residues 672 - 676 (chain A) in PDB entry 4P3N
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with PHE 672 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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614A PHE* 3.6 30.1 - + - -
620A GLN 3.0 8.7 + - - +
621A VAL* 3.3 12.8 - - + -
622A MET* 2.9 24.3 + - - +
670A TYR* 4.2 2.0 - - - +
671A ASN* 1.3 94.2 - - + +
673A ILE* 1.3 63.7 + - - +
674A LEU* 4.1 11.0 - - + -
688A ILE* 3.9 19.3 - - + -
689A ARG 3.7 3.8 - - - +
690A THR* 4.9 2.9 - - + -
696A HIS* 4.6 5.6 - + - -
704A THR* 6.3 0.2 - - + -
708A LEU* 3.5 28.0 - - + -
711A LEU* 4.4 0.2 - - + -
719A ALA* 3.9 29.6 - - + -
720A GLU* 4.1 9.6 - - - -
723A PHE* 3.7 28.5 - + + -
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Residues in contact with ILE 673 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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622A MET* 3.5 13.0 - - + +
624A VAL* 4.3 15.3 - - + -
662A ILE* 4.3 16.4 - - + +
665A ALA* 3.8 24.0 - - + -
666A GLN* 4.0 19.1 - - + +
670A TYR* 3.9 16.4 - - + +
672A PHE* 1.3 78.1 - - - +
674A LEU* 1.3 62.0 + - - +
675A VAL* 3.7 19.0 + - + -
687A ASN 3.4 3.6 - - - +
688A ILE* 3.7 1.4 - - - -
689A ARG* 2.8 42.9 + - + +
690A THR 3.6 25.4 - - - +
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Residues in contact with LEU 674 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621A VAL* 3.7 25.8 - - + -
622A MET 2.9 11.8 + - - +
623A VAL* 3.5 11.4 - - + +
624A VAL 2.9 25.9 + - - +
637A VAL* 4.2 9.0 - - + -
641A PHE* 3.5 37.5 - - + -
672A PHE* 4.6 9.2 - - + -
673A ILE* 1.3 77.9 - - - +
675A VAL* 1.3 63.0 + - - +
676A VAL* 3.9 1.0 + - + -
686A VAL* 4.2 21.1 - - + -
687A ASN 3.6 2.7 - - - -
688A ILE* 4.0 31.9 - - + -
704A THR* 4.6 6.5 - - + -
708A LEU* 5.9 0.2 - - + -
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Residues in contact with VAL 675 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
624A VAL* 3.4 10.1 - - + +
626A VAL* 4.1 11.4 - - + -
658A LEU* 3.9 29.2 - - + -
662A ILE* 4.0 26.0 - - + -
673A ILE* 4.1 14.4 - - + +
674A LEU* 1.3 73.8 - - - +
676A VAL* 1.3 65.4 - - - +
677A GLY 4.2 0.4 - - - -
680A GLU* 4.2 3.1 - - - +
686A VAL* 3.9 0.5 - - - -
687A ASN* 2.9 55.3 + - + +
689A ARG* 5.0 7.9 - - + +
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Residues in contact with VAL 676 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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623A VAL* 4.8 5.2 - - + -
624A VAL 2.9 14.0 + - - +
625A PRO* 3.3 2.2 - - + +
626A VAL* 2.9 29.3 + - - -
630A CYS* 3.9 14.4 - - + +
633A TYR* 3.3 43.7 - - + -
634A ALA* 4.0 21.5 - - + +
637A VAL* 4.3 7.6 - - + -
674A LEU 4.7 4.5 - - - +
675A VAL* 1.3 78.9 - - - +
677A GLY* 1.3 58.0 + - - +
680A GLU* 4.1 1.3 - - - -
685A THR 4.1 2.0 - - - +
686A VAL* 3.9 20.9 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il